.gitattributes
.gitignore
.readthedocs.yaml
CHANGELOG.md
LICENSE
README.md
setup.py
.vscode/settings.json
SyMBac/PSF.py
SyMBac/__init__.py
SyMBac/cell.py
SyMBac/cell_colony.py
SyMBac/cell_geometry.py
SyMBac/general_drawing.py
SyMBac/misc.py
SyMBac/phase_contrast_drawing.py
SyMBac/pySHINE.py
SyMBac/scene_functions.py
SyMBac/trench_geometry.py
SyMBac.egg-info/PKG-INFO
SyMBac.egg-info/SOURCES.txt
SyMBac.egg-info/dependency_links.txt
SyMBac.egg-info/requires.txt
SyMBac.egg-info/top_level.txt
SyMBac/external/__init__.py
SyMBac/external/DeLTA/LICENSE
SyMBac/external/DeLTA/README.md
SyMBac/external/DeLTA/__init__.py
SyMBac/external/DeLTA/all_mother_props_1.pickle
SyMBac/external/DeLTA/all_mother_props_2.pickle
SyMBac/external/DeLTA/bioformats2sequence.py
SyMBac/external/DeLTA/bioformats_env.yml
SyMBac/external/DeLTA/config.py
SyMBac/external/DeLTA/data.py
SyMBac/external/DeLTA/data_structure.txt
SyMBac/external/DeLTA/delta_env.yml
SyMBac/external/DeLTA/model.py
SyMBac/external/DeLTA/pipeline.py
SyMBac/external/DeLTA/segmentation.py
SyMBac/external/DeLTA/segmentation_chambers.py
SyMBac/external/DeLTA/tracking.py
SyMBac/external/DeLTA/train_seg.py
SyMBac/external/DeLTA/train_seg_chambers.py
SyMBac/external/DeLTA/train_track.py
SyMBac/external/DeLTA/utilities.py
SyMBac/sample_images/__init__.py
SyMBac/sample_images/sample_100x.tiff
SyMBac/sample_images/sample_100x_stationary.tiff
docs/Makefile
docs/make.bat
docs/source/Drawing_Phase_Contrast_100x_oil.rst
docs/source/cell_growth_simulation.rst
docs/source/conf.py
docs/source/faqs.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/intro.rst
docs/source/requirements.txt
docs/source/scene_generation.rst
docs/source/symbac_PSF.rst
docs/source/symbac_cell.rst
docs/source/symbac_cell_geometry.rst
docs/source/symbac_general_drawing.rst
docs/source/symbac_misc.rst
docs/source/symbac_phase_contrast_drawing.rst
docs/source/Drawing_Phase_Contrast_100x_oil_files/Drawing_Phase_Contrast_100x_oil_4_1.png
docs/source/docs_notebooks/cell_timeseries_properties.p
docs/source/docs_notebooks/main_segments.p
docs/source/docs_notebooks/run_simulation.ipynb
docs/source/docs_notebooks/scene_generation.ipynb
docs/source/images/index/paper_figures/human_speed_comparison.png
docs/source/images/index/paper_figures/simulation.png
docs/source/images/index/paper_figures/syn_agar_pad.png
docs/source/images/index/paper_figures/syn_mother_machine.png
docs/source/images/index/paper_figures/syn_turbedostat.png
docs/source/images/index/paper_figures/training.png
docs/source/images/scene_generation/PC_PSF.png
docs/source/images/scene_generation/int_and_dims.png
docs/source/images/scene_generation/real_image.png
docs/source/images/scene_generation/scene_example.png
examples/Drawing_Phase_Contrast_100x_oil.ipynb
examples/__init__.py
examples/deep_learning/DeLTA/interactive_preprocess.ipynb
examples/deep_learning/DeLTA/interactive_segment.ipynb
examples/deep_learning/DeLTA/interactive_train_seg.ipynb
examples/deep_learning/DeLTA/interactive_train_seg_multi_training_amount.ipynb
examples/deep_learning/StarDist/stardist_data.ipynb
examples/deep_learning/StarDist/stardist_predict.ipynb
examples/deep_learning/StarDist/stardist_predict_100x_oil.ipynb
examples/deep_learning/StarDist/stardist_training_100x_oil.ipynb
examples/deep_learning/StarDist/stardist_training_Ph2.ipynb
examples/deep_learning/StarDist/test.pdf
examples/deep_learning/StarDist/test_1600_epoch.pdf
examples/deep_learning/StarDist/test_1600_epoch_50perc.pdf
examples/deep_learning/StarDist/test_mixed_cells.png
examples/deep_learning/StarDist/test_nohist.pdf
examples/deep_learning/StarDist/test_nohist.png
readme_files/example_comparison.jpeg
readme_files/image_generation.jpeg
readme_files/speed_comparison.png
readme_files/symbac_sliders.gif
readme_files/training.png
tests/__init__.py
tests/test_phase_contrast_drawing.py